public override Spectrum spectrum(int index, bool getBinaryData)
{
Spectrum s = base.spectrum(index, true);
if (s.cvParam(CVID.MS_MSn_spectrum).empty() ||
(int)s.cvParam(CVID.MS_ms_level).value == 1)
{
if (!getBinaryData)
{
s.binaryDataArrays.Clear();
}
return(s);
}
PrecursorList pl = s.precursors;
BinaryData mzArray = s.getMZArray().data;
BinaryData intensityArray = s.getIntensityArray().data;
PointDataMap <double> mziMap = new PointDataMap <double>();
for (int i = 0; i < (int)s.defaultArrayLength; ++i)
{
mziMap.Insert(mzArray[i], intensityArray[i]);
}
Set <double> pointsToRemove = new Set <double>();
foreach (Precursor p in pl)
{
foreach (SelectedIon si in p.selectedIons)
{
double mz = (double)si.cvParam(CVID.MS_selected_ion_m_z).value;
PointDataMap <double> .Enumerator itr = mziMap.LowerBound(mz - 4.0);
if (itr != null && itr.IsValid)
{
while (itr.IsValid && itr.Current.Key - mz < 4.0)
{
pointsToRemove.Add(itr.Current.Key);
itr.MoveNext();
}
}
CVParam chargeParam = si.cvParam(CVID.MS_charge_state);
if (!chargeParam.empty())
{
int z = (int)chargeParam.value;
for (int i = 1; i < z; ++i)
{
double strippedMz = (mz * z) / (z - i);
itr = mziMap.LowerBound(strippedMz - 4.0);
if (itr != null && itr.IsValid)
{
while (itr.IsValid && itr.Current.Key - strippedMz < 4.0)
{
pointsToRemove.Add(itr.Current.Key);
itr.MoveNext();
}
}
}
}
}
}
if (getBinaryData)
{
mzArray.Clear();
intensityArray.Clear();
foreach (PointDataMap <double> .MapPair pair in mziMap)
{
if (pointsToRemove.Contains(pair.Key))
{
continue;
}
mzArray.Add(pair.Key);
intensityArray.Add(pair.Value);
}
s.defaultArrayLength = (ulong)mzArray.Count;
}
else
{
s.binaryDataArrays.Clear();
s.defaultArrayLength -= (ulong)pointsToRemove.Count;
}
return(s);
}
